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<meta NAME="description" CONTENT="RasMol in Marvin">
<meta NAME="keywords" CONTENT="RasMol, Java, Marvin">
<meta NAME="author" CONTENT="Peter Csizmadia">
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<title>RasMol Scripts in Marvin</title>
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<h1>RasMol Scripts</h1>

<p>
MarvinView can execute scripts containing 3D viewing commands
delimited by semicolons or newlines. Comment lines start with #.
Currently, only the following subset of RasMol/Chime commands is implemented:
<p>
<table CELLSPACING=0 CELLPADDING=4 BORDER=0 id="colored-grid">
<tr VALIGN=TOP>
    <td NOWRAP><code>ballstick</code><br>
	<code>ballstick on</code><br>
	<code>ballstick true</code></td>
    <td>Ball &amp; stick rendering style.<br>
	This command is Marvin-specific.</td>
    </tr>
<tr VALIGN=TOP>
    <td NOWRAP><code>center</code><br>
	<code>center</code> <em>atomno</em><br>
	<code>center [</code><em>x</em><code>, </code><em>y</em><code>,
	    </code><em>z</em><code>]</code><br><br>
	<code>centre</code><br>
	<code>centre</code> <em>atomno</em><br>
	<code>centre [</code><em>x</em><code>, </code><em>y</em><code>,
	    </code><em>z</em><code>]</code><br>
    <td>Defines the center point for the
	<code>rotate</code> and <code>zoom</code> commands.
	Without argument, the center is set to be the center of gravity.
	The argument can be an atom number, or three coordinates specifying
	the distance from the center of gravity.
	The <em>x</em>, <em>y</em>, <em>z</em> values are in RasMol units
	(1/250 Angstrom).
	</td>
    </tr>
<tr VALIGN=TOP>
    <td NOWRAP><code>cpk</code></td>
    <td>Synonymous with <code>spacefill</code>.</td>
    </tr>
<tr VALIGN=TOP>
    <td NOWRAP><code>delay</code><br>
	<code>delay</code> <em>seconds</em></td>
    <td>Delays the continuation of script execution for the specified number of
	seconds. Default delay value is 1 second.
	</td>
    </tr>
<tr VALIGN=TOP>
    <td NOWRAP><code>echo</code> <em>text</em></td>
    <td>Prints a message to the standard output.</td>
    </tr>
<tr VALIGN=TOP>
    <td NOWRAP><code>exit</code></td>
    <td>Exits from the script. In case of nested scripts, it terminates only
	the current level.</td>
    </tr>
<tr VALIGN=TOP>
    <td NOWRAP><a NAME="load"><code>load </code><em>molfile</em></a></td>
    <td>Loads a molecule file from the specified URL.</td>
    </tr>
<tr VALIGN=TOP>
    <td NOWRAP><code>quit</code></td>
    <td>Exits from the script interpreter.
	Terminates all nested levels of scripts.</td>
    </tr>
<tr VALIGN=TOP>
    <td NOWRAP><code>refresh</code></td>
    <td>Redraws the current image. In Marvin, this command is not necessary
	because the image is automatically refreshed at the beginning of
	<code>delay</code> commands and at the end of script.</td></tr>
<tr VALIGN=TOP>
    <td NOWRAP><code>reset</code></td>
    <td>Restores the default viewing transformation.</td></tr>
<tr VALIGN=TOP>
    <td NOWRAP><code>rotate x</code> <em>angle</em><br>
	<code>rotate y</code> <em>angle</em><br>
	<code>rotate z</code> <em>angle</em></td>
    <td>Rotates about the &quot;x&quot;, &quot;y&quot; or &quot;z&quot; axis
	with the specified angle (degrees).</td>
    </tr>
<tr VALIGN=TOP>
    <td NOWRAP><a NAME="script"><code>script </code><em>file</em></a><br>
	<code>source </code><em>file</em></td>
    <td>Reads a script from the specified URL.<br>
	Scripts can be nested without any depth limitation in Marvin.</td>
    </tr>
<tr VALIGN=TOP>
    <td NOWRAP><code>spacefill</code><br>
	<code>spacefill on</code><br>
	<code>spacefill true</code></td>
    <td>Atoms are represented by balls, bonds are not drawn.</td>
    </tr>
<tr VALIGN=TOP>
    <td NOWRAP><code>sticks</code><br>
	<code>sticks on</code><br>
	<code>sticks true</code></td>
    <td>Sticks rendering style.<br>
	This command is Marvin-specific.</td>
    </tr>
<tr VALIGN=TOP>
    <td NOWRAP><code>wireframe</code><br>
	<code>wireframe on</code><br>
	<code>wireframe true</code></td>
    <td>Bonds are represented by lines in wireframe mode.</td>
    </tr>
<tr VALIGN=TOP>
    <td NOWRAP><code>wireknobs</code><br>
	<code>wireknobs on</code><br>
	<code>wireknobs true</code></td>
    <td>Wireframe with knobs.<br>
	This command is Marvin-specific.</td>
    </tr>
<tr VALIGN=TOP>
    <td NOWRAP><code>zap</code></td>
    <td>Deletes molecule and resets parameter
	variables to their default values.</td></tr>
<tr VALIGN=TOP>
    <td NOWRAP><code>zoom</code> <em>percentage</em></td>
    <td>Magnifies to the specified value.</td>
    </tr>
</table>
<p>
<strong>Warning:</strong> RasMol support is incomplete and <em>experimental</em>.

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